A genome sequence of novel SARS-CoV isolates: the genotype, GD-Ins29, leads to a hypothesis of viral transmission in South China

Genomics Proteomics Bioinformatics. 2003 May;1(2):101-7. doi: 10.1016/s1672-0229(03)01014-3.

Abstract

We report a complete genomic sequence of rare isolates (minor genotype) of the SARS-CoV from SARS patients in Guangdong, China, where the first few cases emerged. The most striking discovery from the isolate is an extra 29-nucleotide sequence located at the nucleotide positions between 27,863 and 27,864 (referred to the complete sequence of BJ01) within an overlapped region composed of BGI-PUP5 (BGI-postulated uncharacterized protein 5) and BGI-PUP6 upstream of the N (nucleocapsid) protein. The discovery of this minor genotype, GD-Ins29, suggests a significant genetic event and differentiates it from the previously reported genotype, the dominant form among all sequenced SARS-CoV isolates. A 17-nt segment of this extra sequence is identical to a segment of the same size in two human mRNA sequences that may interfere with viral replication and transcription in the cytosol of the infected cells. It provides a new avenue for the exploration of the virus-host interaction in viral evolution, host pathogenesis, and vaccine development.

Publication types

  • Comparative Study

MeSH terms

  • Base Sequence
  • China
  • Cluster Analysis
  • Gene Components
  • Genetic Variation*
  • Genome, Viral*
  • Genotype
  • Molecular Sequence Data
  • Phylogeny*
  • Reverse Transcriptase Polymerase Chain Reaction
  • SARS Virus / genetics*
  • Sequence Analysis, DNA
  • Severe Acute Respiratory Syndrome / genetics*